Why we have plenty of fish in the sea

HUNTSVILLE, Ala. -- New work from the HudsonAlpha Institute for Biotechnology, with collaborators at Stanford University and five other groups, has pinpointed evolution in action.

By determining genomic sequence from many groups of stickleback fish, the scientists were able to show specific genomic changes leading to the ability of different fish populations to adapt to new environments. "We were pleased with the ability of genomics to show us what molecular changes are important in evolutionary processes," said Richard Myers, Ph.D., president and director of HudsonAlpha.

At the end of the last ice age, marine stickleback fish were present in many waters and then became separated into different populations in lakes and streams worldwide. These populations evolved separate traits, such as number of spines, body length or eye size, which allowed them to thrive in their specific habitat.

To tie these traits to specific DNA changes, the scientists generated a reference of the threespine stickleback fish genome at high quality. "With our reference genome and genetic map for stickleback, we will now be able to use it as a model organism for future studies of adaptation and environmental selection," said HudsonAlpha faculty investigator Jeremy Schmutz.

Scientists then sequenced 21 pairs of fish that varied at different traits and compared them to each other and to the reference fish genome. Small regions of the fish genome stood out due to changes in the genomic DNA, and many of these could be related to how the fish look and behave.

Two interesting findings stood out. First, the changes between fish populations often happened not by mutations in single DNA bases, but by inversions of very large chunks of DNA on fish chromosomes. When these large inversions of DNA occur, fish can no longer breed with each other effectively and start to become separate species.

Second, the scientists saw that when evolution allowing fish to adapt to their environment seemed to come from single DNA base changes, these were most often in regions of the genome that regulate genes and proteins, instead of in the genes themselves. In contrast, previous work has shown that in laboratory or domesticated animals, changes in genes and proteins are found more often.

Jane Grimwood, Ph.D., also a faculty investigator at HudsonAlpha, explained, "The predominance of regulatory changes in the evolution of sticklebacks suggests that natural populations may behave differently than domesticated animals, and our genetic mapping of many species will advance similar studies in natural and wild organisms."

HudsonAlpha researchers have been part of the NHGRI - NIH funded Center for Excellence in Genome Sciences, or CEGS, project for developing stickleback as a model organism since 2002. As part of this effort, they and colleagues at Stanford University have produced genomic resources for several freshwater and marine stickleback fish. Currently, the HudsonAlpha Genome Sequencing Center is building a reference sequence for the Y chromosome for stickleback, as the sequenced fish was a female.

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The paper "The genomic basis of adaptive evolution in threespine sticklebacks" will be published in the 4 April 2012 issue of the journal Nature and available at www.nature.com/nature.

The HudsonAlpha Institute for Biotechnology in Huntsville, Ala, is the cornerstone of the Cummings Research Park Biotechnology Campus. The campus hosts a synergistic cluster of life sciences talent - science, education and business professionals - that promises collaborative innovation to turn knowledge and ideas into commercial products and services for improving human health and strengthening Alabama's progressively diverse economy. The non-profit institute is housed in a state-of-the-art, 270,000 square-ft. facility strategically located in the nation's second largest research park. HudsonAlpha has a three-fold mission of genomic research, economic development and educational outreach.

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